Added sample merging to RNA-seq pipeline

Can now specify sets of samples to merge in addition to keeping all
samples separate
CommandLineParser returns primitive types
CommandLineParser takes primitive types as argument default values
Merge branch 'master' of https://github.com/mgarber/scriptureV2
Minor additions to CommandLineParser
Method to get the spliced sequence of a transcript
Added an overlaps() method with option of ignoring orientation
Implemented equals and compareTo
More helpful logging
Option to specify line length for writers in FastaSequenceIO